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Author

Nathalie Choisne

Bio: Nathalie Choisne is an academic researcher from Université Paris-Saclay. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 17, co-authored 30 publications receiving 9003 citations. Previous affiliations of Nathalie Choisne include Institut national de la recherche agronomique.
Topics: Genome, Gene, Genomics, Reference genome, Synteny

Papers
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Journal ArticleDOI
Takashi Matsumoto1, Jianzhong Wu1, Hiroyuki Kanamori1, Yuichi Katayose1  +262 moreInstitutions (25)
11 Aug 2005-Nature
TL;DR: A map-based, finished quality sequence that covers 95% of the 389 Mb rice genome, including virtually all of the euchromatin and two complete centromeres, and finds evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes.
Abstract: Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

3,423 citations

Journal ArticleDOI
26 Aug 2007-Nature
TL;DR: A high-quality draft of the genome sequence of grapevine is obtained from a highly homozygous genotype, revealing the contribution of three ancestral genomes to the grapevine haploid content and explaining the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
Abstract: The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

3,311 citations

Journal ArticleDOI
Nevin D. Young1, Frédéric Debellé2, Frédéric Debellé3, Giles E. D. Oldroyd4, René Geurts5, Steven B. Cannon6, Steven B. Cannon7, Michael K. Udvardi, Vagner A. Benedito8, Klaus F. X. Mayer, Jérôme Gouzy3, Jérôme Gouzy2, Heiko Schoof9, Yves Van de Peer10, Sebastian Proost10, Douglas R. Cook11, Blake C. Meyers12, Manuel Spannagl, Foo Cheung13, Stéphane De Mita5, Vivek Krishnakumar13, Heidrun Gundlach, Shiguo Zhou14, Joann Mudge15, Arvind K. Bharti15, Jeremy D. Murray4, Marina Naoumkina, Benjamin D. Rosen11, Kevin A. T. Silverstein1, Haibao Tang13, Stephane Rombauts10, Patrick X. Zhao, Peng Zhou1, Valérie Barbe, Philippe Bardou3, Philippe Bardou2, Michael Bechner14, Arnaud Bellec3, Anne Berger, Hélène Bergès3, Shelby L. Bidwell13, Ton Bisseling5, Ton Bisseling16, Nathalie Choisne, Arnaud Couloux, Roxanne Denny1, Shweta Deshpande17, Xinbin Dai, Jeff J. Doyle18, Anne Marie Dudez3, Anne Marie Dudez2, Andrew Farmer15, Stéphanie Fouteau, Carolien Franken5, Chrystel Gibelin3, Chrystel Gibelin2, John Gish11, Steven A. Goldstein14, Alvaro J. González12, Pamela J. Green12, Asis Hallab19, Marijke Hartog5, Axin Hua17, Sean Humphray20, Dong-Hoon Jeong12, Yi Jing17, Anika Jöcker19, Steve Kenton17, Dong-Jin Kim11, Dong-Jin Kim21, Kathrin Klee19, Hongshing Lai17, Chunting Lang5, Shaoping Lin17, Simone L. Macmil17, Ghislaine Magdelenat, Lucy Matthews20, Jamison McCorrison13, Erin L. Monaghan13, Jeong Hwan Mun22, Jeong Hwan Mun11, Fares Z. Najar17, Christine Nicholson20, Céline Noirot3, Majesta O'Bleness17, Charles Paule1, Julie Poulain, Florent Prion2, Florent Prion3, Baifang Qin17, Chunmei Qu17, Ernest F. Retzel15, Claire Riddle20, Erika Sallet2, Erika Sallet3, Sylvie Samain, Nicolas Samson3, Nicolas Samson2, Iryna Sanders17, Olivier Saurat2, Olivier Saurat3, Claude Scarpelli, Thomas Schiex3, Béatrice Segurens, Andrew J. Severin7, D. Janine Sherrier12, Ruihua Shi17, Sarah Sims20, Susan R. Singer23, Senjuti Sinharoy, Lieven Sterck10, Agnès Viollet, Bing Bing Wang1, Keqin Wang17, Mingyi Wang, Xiaohong Wang1, Jens Warfsmann19, Jean Weissenbach, Doug White17, James D. White17, Graham B. Wiley17, Patrick Wincker, Yanbo Xing17, Limei Yang17, Ziyun Yao17, Fu Ying17, Jixian Zhai12, Liping Zhou17, Antoine Zuber2, Antoine Zuber3, Jean Dénarié3, Jean Dénarié2, Richard A. Dixon, Gregory D. May15, David C. Schwartz14, Jane Rogers24, Francis Quetier, Christopher D. Town13, Bruce A. Roe17 
22 Dec 2011-Nature
TL;DR: The draft sequence of the M. truncatula genome sequence is described, a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics, which provides significant opportunities to expand al falfa’s genomic toolbox.
Abstract: Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.

1,153 citations

Journal ArticleDOI
TL;DR: High-quality de novo assembly of the apple genome is produced and genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
Abstract: Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

588 citations

Journal ArticleDOI
TL;DR: The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
Abstract: Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.

350 citations


Cited by
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI
14 Dec 2000-Nature
TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
Abstract: The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

8,742 citations

Journal ArticleDOI
TL;DR: Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements.
Abstract: We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.

8,315 citations

Journal ArticleDOI
14 Jan 2010-Nature
TL;DR: An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
Abstract: Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

3,743 citations

Journal ArticleDOI
TL;DR: Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number of complete plant genomes.
Abstract: The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

3,728 citations